LD data from CEU hg18
收藏Zenodo2020-07-30 更新2026-05-25 收录
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https://zenodo.org/record/3560541
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LD data from CEU hg18, based on ftp://ftp.ncbi.nlm.nih.gov/hapmap/ld_data/latest Algo for computing: import pandas as pd rule ld_blocks:<br> input:<br> expand("blocks/{chromosome}_blocks.gz", chromosome=["chr{}".format(c) for c in list(range(1, 23)) + ["X"]]) rule get_blocks:<br> output:<br> "blocks/{chromosome}_blocks.gz"<br> run: c = wildcards.chromosome<br> f = r"ftp://ftp.ncbi.nlm.nih.gov/hapmap/ld_data/latest/ld_{}_CEU.txt.gz".format(c)<br> print(f)<br> df = pd.read_csv(f,<br> sep=" ", header=None, usecols=[0, 1, 8])<br> print(df.head()) df.columns = "Start End Block".split()<br> ls = df.groupby("Block").agg({"Start": "first", "End": "last", "Block": ["first", "count"]}).reset_index(drop=True)<br> ls.columns = "Start End LDBlock Count".split()<br> lengths = ls["End"] - ls["Start"]<br> ls.insert(ls.shape[1], "Length", lengths)<br> ls.insert(0, "Chromosome", c) ls.to_csv(output[0], sep="\t", index=None)<br>
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Zenodo创建时间：
2019-12-03
